SCOTLAND’S most senior official has defended the civil service’s work on Scottish independence and said the government will continue to seek a Section 30 order to allow for a "lawful" indyref2. 

Permanent Secretary John Paul Marks also suggested the current constitutional stalemate could change after the next general election. 

The mandarin has come under pressure in recent weeks, with UK Government ministers questioning the "constitutional propriety" of his team taking orders from Jamie Hepburn, the new minister for independence. 

READ MORE: Humza Yousaf's top official faces Holyrood quiz on independence work

Humza Yousaf created the post shortly after his victory in the SNP leadership contest, prompting Labour peer George Foulkes to ask the UK government about the legality of taxpayer's money being used to fund the role. 

Alister Jack told the peer he had written to the UK’s most senior civil servant, Cabinet Secretary Simon Case to “advise on the constitutional propriety of appointing this ministerial role" in light of the Supreme Court case which categorically said Holyrood could not hold a referendum without the consent of Westminster. 

The Scottish Secretary also sought assurance "that no UK civil servant will be engaged in this new department.” 

The new role was first mooted by Mr Yousaf after his leadership contest rival Kate Forbes suggested the responsibility for building the prospectus for independence be taken away from the civil service.

Mr Yousaf said: "Why on Earth would you not use the machinery of government to fund the cause?”

READ MORE: Alister Jack questions 'constitutional propriety' of new indy minister

Asked about Mr Jack’s involvement, Mr Marks told Holyrood’s Finance and Public Administration Committee: "It is for the First Minister to appoint his ministerial team, given his priorities, and that ministerial team is then voted on by this parliament, and then it is for the civil service to serve that ministerial team with impartiality.

"We serve the government of the day. 

“That includes with regards to constitutional reform, and it has been well understood under devolution for many years that the civil service in the Scottish Government serves the Scottish Government and their priorities and we provide policy advice, including the development of prospectus paper series for this government to set out its constitutional objectives."

He said the issue was "not just a theoretical debate or a strategic long-term debate, it is a here-and-now reality."

Mr Marks added: "From my perspective, there are very clear, proper and regular grounds for the First Minister to appoint his ministerial team.

"It is necessary for the civil service to serve that ministerial team with impartiality and there is a clear set of constitutional priorities here and now which need advising on and tackling, because if we're going to deliver this government's programme, whether it be on ScotWind, the Deposit Return Scheme or a number of other energy reforms and equality reforms, we need to continue to influence and engage with the UK Government with regards to the devolution settlement and the constitution.

Mr Marks added: "And so, to an extent, it is important that I have the capability in the civil service in Scotland equipped to serve ministers in this government, not just now, but also recognising that things can change in the future. 

"We'll continue to seek a Section 30 Order so that any referendum would always be on lawful grounds as per the last referendum in Scotland, but also recognising UK General Election in 24/25, and clearly the future of the constitution of the UK could change again, and we need to have a capability ready to respond.”

READ MORE: Humza Yousaf names new 'minister for independence'

Under Nicola Sturgeon, the Scottish Government began publishing a new multi-part prospectus, Building a New Scotland, in June last year, with two further parts in July and October.

The fourth Scottish Government prospectus on independence is reportedly due to be published in the next few weeks. 

During the SNP leadership contest, Mr Yousaf criticised the documents saying they were material “that frankly sits on a website and nobody reads”.

In November, it emerged 25 civil servants costing up to £1.5m a year in wages were working on the Scottish Government prospectus, including one paid up to £83,000.

Responding to the evidence from Mr Marks, a UK Government source said: "The Scottish Government and their officials have an interest in the constitution in so much as they should respect the devolution settlement.

"However, the constitution is clearly reserved and there is a legitimate question to be asked about whether Scottish Government civil servants should be working on the SNP's political mission to remove Scotland from the UK.

Scottish Liberal Democrat MSP Willie Rennie said: “Just because civil servants can work on independence doesn’t mean they should.  

“These independence papers are a colossal waste of money and a colossal waste of trees.  

“Instead, the Scottish Government should be focussed on helping the 1 in 7 Scots on an NHS waiting list, tackling the cost-of-living crisis and stopping sewage pouring into our rivers.”

Earlier in the session, Deoputy First Minister Shona Robison told the committee that decision-making in the Scottish Government can be “frustratingly long”.

MSPs on the cross-party committee have already been told by former officials the decision-making process is “rushed, unclear and unstructured”, something which was put to Ms Robison on Tuesday.

But she said: “It’s not been my experience, I have to say.

“Sometimes it can feel the opposite, that decisions sometimes can be frustratingly long to make.”

Advice and discussions can take some time “even when there’s an eagerness to go on and do what’s in front of you”, she said.

Saying she had been in government on and off for 15 years, Ms Robison said: “When you gain confidence and experience as a minister, that enables you to make decisions perhaps more quickly and actually to be able to challenge the advice that comes in front of you a bit more readily than a minister that perhaps doesn’t have that experience and might quite rightly take longer.”

The committee’s convener Michael Marra asked her what lessons were learned about the government’s gender recognition legislation.

Ms Robison led this Bill through Holyrood when she was social justice secretary.

She said: “One of my reflections is – was there a way of trying to build more of a consensus around the issue that I felt very strongly was important to try and do.

“Could we have done that at an earlier stage, was it possible?”

Finding consensus became difficult due to the increasingly polarised nature of the debate, she said.